Sample contamination detection of contaminated fragments with cpg-snp contamination markers

EP4562186A4Pending Publication Date: 2026-06-24GRAIL INC
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Patent Information

Authority / Receiving Office
EP · EP
Patent Type
Applications
Current Assignee / Owner
GRAIL INC
Filing Date
2023-07-24
Publication Date
2026-06-24

AI Technical Summary

Technical Problem

Current methods for detecting contamination in cell-free DNA samples used for cancer diagnosis are inadequate, leading to inaccurate results due to foreign DNA fragments from other individuals or organisms, which can skew cancer detection models and hinder early disease detection.

Method used

The use of CpG single nucleotide polymorphism (SNP) contamination markers to identify and filter out contaminated DNA fragments by comparing sequence reads to a reference genome, determining the presence of contamination based on homozygous haplotype discrepancies and threshold numbers, thereby ensuring accurate cancer prediction.

Benefits of technology

This approach significantly improves the accuracy of cancer detection by effectively removing contaminated DNA fragments, reducing errors in sequencing data, and enhancing the reliability of cancer classification models.

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Abstract

Methods and systems for detecting contaminated fragments in a biological sample for cancer classification are disclosed. The system identifies CpG-SNP contamination markers. The CpG-SNP contamination markers include at least one SNP that affects a CpG site. The CpG-SNP contamination markers may include additive CpG-SNP sites and / or subtractive CpG-SNP sites. Additive CpG-SNP sites include an SNP that creates a new CpG site. Subtractive CpG-SNP sites include an SNP that removes a preexisting CpG site. Hybrid sites may include additional sites. A multiple CpG-SNP contamination marker comprises two or more CpG-SNP sites. A CpG-SNP & indel contamination marker comprises at least one CpG-SNP site and an indel site. For a given sample, the system identifies contamination markers for which the sample is homozygous. The system determines fragments having a haplotype that is different from the homozygous haplotype of the sample to be contamination fragments.
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